We propose to generate moderate to low-resolution tertiary structures of proteins using data obtained by chemical cross-linking MS-based experiments in conjunction with protein modeling and theory. This is a joint project involving groups from Chiron Corporation and UCSF. Specifically, we will need mass spectrometry to help identify peptides that are crosslinked via homo- or heterobifunctional reagents after proteolytic digestion. In some cases, identities will be assigned by relatively accurate mass measurements (better than 50 ppm) and MS/MS experiments such as post-source decay (PSD). We propose to use these structures in structure-based drug design.